Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 02:49:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/10_2023/7dkj_30707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/10_2023/7dkj_30707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/10_2023/7dkj_30707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/10_2023/7dkj_30707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/10_2023/7dkj_30707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/10_2023/7dkj_30707.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12633 2.51 5 N 3381 2.21 5 O 3984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 36": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A ASP 455": "OD1" <-> "OD2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "D ASP 1": "OD1" <-> "OD2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "E GLU 252": "OE1" <-> "OE2" Residue "E TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ASP 373": "OD1" <-> "OD2" Residue "E ASP 455": "OD1" <-> "OD2" Residue "E GLU 459": "OE1" <-> "OE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ASP 53": "OD1" <-> "OD2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 151": "OE1" <-> "OE2" Residue "H ASP 1": "OD1" <-> "OD2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "I ARG 134": "NH1" <-> "NH2" Residue "I GLU 213": "OE1" <-> "OE2" Residue "I GLU 228": "OE1" <-> "OE2" Residue "I GLU 252": "OE1" <-> "OE2" Residue "I TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 338": "OE1" <-> "OE2" Residue "I ASP 373": "OD1" <-> "OD2" Residue "I ASP 455": "OD1" <-> "OD2" Residue "I GLU 459": "OE1" <-> "OE2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K ASP 53": "OD1" <-> "OD2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "K TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 151": "OE1" <-> "OE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 20112 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "C" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "D" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "E" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "G" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "H" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "I" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "K" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "L" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.28, per 1000 atoms: 0.51 Number of scatterers: 20112 At special positions: 0 Unit cell: (154.35, 149.94, 148.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 3984 8.00 N 3381 7.00 C 12633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 464 " distance=2.03 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 69 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 303 " distance=2.02 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS D 147 " distance=1.92 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 464 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 69 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 303 " distance=2.02 Simple disulfide: pdb=" SG CYS E 471 " - pdb=" SG CYS E 475 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS H 147 " distance=1.97 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 464 " distance=2.03 Simple disulfide: pdb=" SG CYS I 44 " - pdb=" SG CYS I 275 " distance=2.03 Simple disulfide: pdb=" SG CYS I 57 " - pdb=" SG CYS I 69 " distance=2.03 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 136 " distance=2.03 Simple disulfide: pdb=" SG CYS I 279 " - pdb=" SG CYS I 303 " distance=2.02 Simple disulfide: pdb=" SG CYS I 471 " - pdb=" SG CYS I 475 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS K 121 " - pdb=" SG CYS L 147 " distance=2.21 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 13 " " NAG A 602 " - " ASN A 25 " " NAG A 603 " - " ASN A 287 " " NAG B 1 " - " ASN A 166 " " NAG E 601 " - " ASN E 13 " " NAG E 602 " - " ASN E 25 " " NAG E 603 " - " ASN E 287 " " NAG F 1 " - " ASN A 481 " " NAG I 601 " - " ASN I 13 " " NAG I 602 " - " ASN I 25 " " NAG I 603 " - " ASN I 287 " " NAG J 1 " - " ASN E 166 " " NAG M 1 " - " ASN E 481 " " NAG N 1 " - " ASN I 166 " " NAG O 1 " - " ASN I 481 " Time building additional restraints: 8.92 Conformation dependent library (CDL) restraints added in 2.6 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 45 sheets defined 28.1% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 58 through 65 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 364 through 386 Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 453 removed outlier: 3.938A pdb=" N LEU A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 Processing helix chain 'A' and resid 485 through 499 removed outlier: 3.825A pdb=" N TYR A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.841A pdb=" N ASN C 56 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 133 through 170 Proline residue: C 146 - end of helix Proline residue: C 165 - end of helix Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Proline residue: D 132 - end of helix Proline residue: D 151 - end of helix removed outlier: 3.715A pdb=" N LYS D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 99 through 108 Processing helix chain 'E' and resid 184 through 193 Processing helix chain 'E' and resid 364 through 386 Processing helix chain 'E' and resid 398 through 400 No H-bonds generated for 'chain 'E' and resid 398 through 400' Processing helix chain 'E' and resid 401 through 453 removed outlier: 3.939A pdb=" N LEU E 426 " --> pdb=" O ASN E 422 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 481 Processing helix chain 'E' and resid 485 through 499 removed outlier: 3.824A pdb=" N TYR E 489 " --> pdb=" O ASP E 485 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU E 491 " --> pdb=" O PRO E 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 3.842A pdb=" N ASN G 56 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'G' and resid 76 through 78 No H-bonds generated for 'chain 'G' and resid 76 through 78' Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 133 through 170 Proline residue: G 146 - end of helix Proline residue: G 165 - end of helix Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN H 124 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP H 131 " --> pdb=" O LEU H 127 " (cutoff:3.500A) Proline residue: H 132 - end of helix Proline residue: H 151 - end of helix removed outlier: 3.715A pdb=" N LYS H 159 " --> pdb=" O ALA H 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 65 Processing helix chain 'I' and resid 99 through 108 Processing helix chain 'I' and resid 184 through 193 Processing helix chain 'I' and resid 364 through 386 Processing helix chain 'I' and resid 398 through 400 No H-bonds generated for 'chain 'I' and resid 398 through 400' Processing helix chain 'I' and resid 401 through 453 removed outlier: 3.938A pdb=" N LEU I 426 " --> pdb=" O ASN I 422 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE I 437 " --> pdb=" O ARG I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 481 Processing helix chain 'I' and resid 485 through 499 removed outlier: 3.825A pdb=" N TYR I 489 " --> pdb=" O ASP I 485 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU I 491 " --> pdb=" O PRO I 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU I 492 " --> pdb=" O LYS I 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU I 499 " --> pdb=" O LEU I 495 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 57 removed outlier: 3.841A pdb=" N ASN K 56 " --> pdb=" O ASP K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 67 Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'K' and resid 133 through 170 Proline residue: K 146 - end of helix Proline residue: K 165 - end of helix Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) Proline residue: L 132 - end of helix Proline residue: L 151 - end of helix removed outlier: 3.715A pdb=" N LYS L 159 " --> pdb=" O ALA L 155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS A 45 " --> pdb=" O THR A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.817A pdb=" N ILE A 81 " --> pdb=" O ILE A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 112 through 117 removed outlier: 6.737A pdb=" N HIS A 112 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A 253 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 117 removed outlier: 6.737A pdb=" N HIS A 112 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A 253 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 161 through 165 Processing sheet with id=AA9, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AB1, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.026A pdb=" N ILE C 80 " --> pdb=" O ASP C 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS C 98 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP C 112 " --> pdb=" O CYS C 98 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG C 100 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AB8, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS E 45 " --> pdb=" O THR E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 83 removed outlier: 6.819A pdb=" N ILE E 81 " --> pdb=" O ILE E 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS E 112 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE E 176 " --> pdb=" O TYR E 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE E 176 " --> pdb=" O PRO E 251 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS E 112 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE E 176 " --> pdb=" O TYR E 253 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 161 through 165 Processing sheet with id=AC6, first strand: chain 'E' and resid 292 through 293 Processing sheet with id=AC7, first strand: chain 'E' and resid 457 through 458 Processing sheet with id=AC8, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.025A pdb=" N ILE G 80 " --> pdb=" O ASP G 75 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.609A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS G 98 " --> pdb=" O TRP G 112 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP G 112 " --> pdb=" O CYS G 98 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG G 100 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.609A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AD5, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AD6, first strand: chain 'I' and resid 32 through 33 Processing sheet with id=AD7, first strand: chain 'I' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS I 45 " --> pdb=" O THR I 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'I' and resid 81 through 83 removed outlier: 6.818A pdb=" N ILE I 81 " --> pdb=" O ILE I 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS I 112 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR I 253 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE I 176 " --> pdb=" O TYR I 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE I 176 " --> pdb=" O PRO I 251 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS I 112 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR I 253 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE I 176 " --> pdb=" O TYR I 253 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 161 through 165 Processing sheet with id=AE3, first strand: chain 'I' and resid 292 through 293 Processing sheet with id=AE4, first strand: chain 'I' and resid 457 through 458 Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.025A pdb=" N ILE K 80 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET K 34 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS K 98 " --> pdb=" O TRP K 112 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP K 112 " --> pdb=" O CYS K 98 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG K 100 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET K 34 " --> pdb=" O PHE K 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'L' and resid 53 through 54 822 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.43 Time building geometry restraints manager: 9.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6501 1.34 - 1.46: 4648 1.46 - 1.58: 9233 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 20550 Sorted by residual: bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.570 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" CG1 ILE A 383 " pdb=" CD1 ILE A 383 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.29e+00 bond pdb=" CG1 ILE E 383 " pdb=" CD1 ILE E 383 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.25e+00 ... (remaining 20545 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.53: 337 105.53 - 112.65: 10725 112.65 - 119.77: 6880 119.77 - 126.89: 9576 126.89 - 134.01: 277 Bond angle restraints: 27795 Sorted by residual: angle pdb=" CA GLN K 78 " pdb=" CB GLN K 78 " pdb=" CG GLN K 78 " ideal model delta sigma weight residual 114.10 124.54 -10.44 2.00e+00 2.50e-01 2.72e+01 angle pdb=" CA GLN C 78 " pdb=" CB GLN C 78 " pdb=" CG GLN C 78 " ideal model delta sigma weight residual 114.10 124.53 -10.43 2.00e+00 2.50e-01 2.72e+01 angle pdb=" CA GLN G 78 " pdb=" CB GLN G 78 " pdb=" CG GLN G 78 " ideal model delta sigma weight residual 114.10 124.52 -10.42 2.00e+00 2.50e-01 2.71e+01 angle pdb=" CB GLN C 78 " pdb=" CG GLN C 78 " pdb=" CD GLN C 78 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.70e+00 3.46e-01 1.41e+01 angle pdb=" CB GLN K 78 " pdb=" CG GLN K 78 " pdb=" CD GLN K 78 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.70e+00 3.46e-01 1.41e+01 ... (remaining 27790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 10686 17.86 - 35.71: 1087 35.71 - 53.57: 232 53.57 - 71.42: 75 71.42 - 89.28: 46 Dihedral angle restraints: 12126 sinusoidal: 4974 harmonic: 7152 Sorted by residual: dihedral pdb=" CB CYS E 44 " pdb=" SG CYS E 44 " pdb=" SG CYS E 275 " pdb=" CB CYS E 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.61 -76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS I 44 " pdb=" SG CYS I 44 " pdb=" SG CYS I 275 " pdb=" CB CYS I 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.62 -76.38 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS A 44 " pdb=" SG CYS A 44 " pdb=" SG CYS A 275 " pdb=" CB CYS A 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.64 -76.36 1 1.00e+01 1.00e-02 7.34e+01 ... (remaining 12123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2846 0.097 - 0.194: 190 0.194 - 0.291: 9 0.291 - 0.387: 0 0.387 - 0.484: 3 Chirality restraints: 3048 Sorted by residual: chirality pdb=" C1 NAG I 602 " pdb=" ND2 ASN I 25 " pdb=" C2 NAG I 602 " pdb=" O5 NAG I 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 25 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 25 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 ... (remaining 3045 not shown) Planarity restraints: 3582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO D 95 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR L 94 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO L 95 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 94 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO H 95 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO H 95 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 95 " 0.040 5.00e-02 4.00e+02 ... (remaining 3579 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 348 2.62 - 3.19: 19418 3.19 - 3.76: 31253 3.76 - 4.33: 43362 4.33 - 4.90: 71032 Nonbonded interactions: 165413 Sorted by model distance: nonbonded pdb=" OG1 THR E 128 " pdb=" OG1 THR E 152 " model vdw 2.056 2.440 nonbonded pdb=" OG1 THR A 128 " pdb=" OG1 THR A 152 " model vdw 2.056 2.440 nonbonded pdb=" OG1 THR I 128 " pdb=" OG1 THR I 152 " model vdw 2.056 2.440 nonbonded pdb=" NZ LYS L 39 " pdb=" O GLU L 81 " model vdw 2.090 2.520 nonbonded pdb=" NZ LYS D 39 " pdb=" O GLU D 81 " model vdw 2.090 2.520 ... (remaining 165408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.060 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 53.040 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 20550 Z= 0.485 Angle : 0.873 10.440 27795 Z= 0.463 Chirality : 0.054 0.484 3048 Planarity : 0.005 0.072 3567 Dihedral : 16.083 89.281 7485 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.84 % Allowed : 2.26 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.16), residues: 2472 helix: -1.01 (0.20), residues: 597 sheet: -1.31 (0.22), residues: 567 loop : -1.91 (0.16), residues: 1308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 418 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 7 residues processed: 444 average time/residue: 0.3253 time to fit residues: 218.6188 Evaluate side-chains 324 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 317 time to evaluate : 2.244 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3788 time to fit residues: 6.8858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 62 optimal weight: 30.0000 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 220 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 353 HIS C 13 GLN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 353 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN E 408 ASN ** G 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 146 GLN I 194 ASN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN I 377 ASN ** K 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20550 Z= 0.210 Angle : 0.670 8.650 27795 Z= 0.350 Chirality : 0.046 0.395 3048 Planarity : 0.005 0.055 3567 Dihedral : 5.567 38.080 2700 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.94 % Allowed : 11.57 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2472 helix: 0.71 (0.22), residues: 594 sheet: -1.25 (0.21), residues: 564 loop : -1.76 (0.16), residues: 1314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 347 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 368 average time/residue: 0.3087 time to fit residues: 176.4495 Evaluate side-chains 314 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 291 time to evaluate : 2.172 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1905 time to fit residues: 11.0539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 150 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 238 optimal weight: 20.0000 chunk 196 optimal weight: 0.6980 chunk 219 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN G 157 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 GLN ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS K 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20550 Z= 0.213 Angle : 0.617 8.716 27795 Z= 0.320 Chirality : 0.046 0.383 3048 Planarity : 0.004 0.059 3567 Dihedral : 5.273 36.252 2700 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.66 % Allowed : 14.02 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2472 helix: 1.24 (0.22), residues: 594 sheet: -1.09 (0.22), residues: 528 loop : -1.70 (0.16), residues: 1350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 312 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 338 average time/residue: 0.3003 time to fit residues: 158.8437 Evaluate side-chains 294 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 279 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2034 time to fit residues: 8.6620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 20.0000 chunk 166 optimal weight: 0.0980 chunk 114 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 148 optimal weight: 30.0000 chunk 221 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 ASN E 377 ASN E 469 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 GLN L 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20550 Z= 0.279 Angle : 0.642 11.680 27795 Z= 0.331 Chirality : 0.046 0.396 3048 Planarity : 0.004 0.061 3567 Dihedral : 5.249 36.642 2700 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.07 % Allowed : 16.51 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2472 helix: 1.25 (0.21), residues: 594 sheet: -1.31 (0.22), residues: 558 loop : -1.70 (0.16), residues: 1320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 298 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 31 residues processed: 328 average time/residue: 0.3108 time to fit residues: 158.1138 Evaluate side-chains 310 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 279 time to evaluate : 2.239 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1888 time to fit residues: 13.9079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20550 Z= 0.257 Angle : 0.620 11.397 27795 Z= 0.320 Chirality : 0.046 0.393 3048 Planarity : 0.004 0.062 3567 Dihedral : 5.153 36.679 2700 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.06 % Allowed : 19.27 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2472 helix: 1.25 (0.21), residues: 597 sheet: -1.35 (0.22), residues: 558 loop : -1.62 (0.16), residues: 1317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 312 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 326 average time/residue: 0.3177 time to fit residues: 160.3334 Evaluate side-chains 303 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 285 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2027 time to fit residues: 9.6740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 8.9990 chunk 211 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN E 408 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 GLN L 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20550 Z= 0.328 Angle : 0.671 13.591 27795 Z= 0.345 Chirality : 0.047 0.405 3048 Planarity : 0.005 0.065 3567 Dihedral : 5.265 37.391 2700 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.98 % Allowed : 19.59 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.17), residues: 2472 helix: 1.04 (0.21), residues: 606 sheet: -1.39 (0.21), residues: 579 loop : -1.73 (0.16), residues: 1287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 309 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 27 residues processed: 334 average time/residue: 0.3229 time to fit residues: 167.1019 Evaluate side-chains 301 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 274 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1989 time to fit residues: 13.0597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 234 optimal weight: 30.0000 chunk 146 optimal weight: 30.0000 chunk 142 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN H 79 GLN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 20550 Z= 0.428 Angle : 0.736 11.417 27795 Z= 0.379 Chirality : 0.050 0.423 3048 Planarity : 0.005 0.064 3567 Dihedral : 5.600 39.123 2700 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.75 % Allowed : 20.29 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2472 helix: 0.86 (0.21), residues: 606 sheet: -1.42 (0.22), residues: 552 loop : -1.79 (0.16), residues: 1314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 301 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 330 average time/residue: 0.3091 time to fit residues: 160.0589 Evaluate side-chains 297 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 277 time to evaluate : 2.298 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2057 time to fit residues: 10.5214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 148 optimal weight: 40.0000 chunk 159 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 20550 Z= 0.238 Angle : 0.645 14.179 27795 Z= 0.331 Chirality : 0.046 0.397 3048 Planarity : 0.005 0.063 3567 Dihedral : 5.346 38.062 2700 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.97 % Allowed : 20.84 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.17), residues: 2472 helix: 1.08 (0.21), residues: 609 sheet: -1.49 (0.22), residues: 561 loop : -1.69 (0.17), residues: 1302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 303 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 317 average time/residue: 0.3109 time to fit residues: 154.0045 Evaluate side-chains 293 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 277 time to evaluate : 2.153 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1861 time to fit residues: 8.6408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 30.0000 chunk 204 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20550 Z= 0.229 Angle : 0.633 12.308 27795 Z= 0.325 Chirality : 0.046 0.390 3048 Planarity : 0.004 0.062 3567 Dihedral : 5.204 36.915 2700 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.32 % Allowed : 21.85 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2472 helix: 1.17 (0.21), residues: 609 sheet: -1.39 (0.22), residues: 549 loop : -1.66 (0.17), residues: 1314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 296 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 299 average time/residue: 0.3009 time to fit residues: 139.8593 Evaluate side-chains 281 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 276 time to evaluate : 2.056 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1761 time to fit residues: 4.5025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 222 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20550 Z= 0.275 Angle : 0.653 12.011 27795 Z= 0.334 Chirality : 0.046 0.394 3048 Planarity : 0.005 0.062 3567 Dihedral : 5.247 36.627 2700 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.37 % Allowed : 22.04 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2472 helix: 1.19 (0.21), residues: 606 sheet: -1.39 (0.22), residues: 549 loop : -1.66 (0.17), residues: 1317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 285 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 290 average time/residue: 0.2984 time to fit residues: 137.0323 Evaluate side-chains 278 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 274 time to evaluate : 2.142 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1870 time to fit residues: 4.3348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 177 optimal weight: 0.9980 chunk 28 optimal weight: 0.0070 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 169 optimal weight: 0.0670 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 ASN E 377 ASN E 477 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.182202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.172521 restraints weight = 26103.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.170431 restraints weight = 43165.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.169825 restraints weight = 63166.485| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20550 Z= 0.174 Angle : 0.609 11.360 27795 Z= 0.313 Chirality : 0.045 0.370 3048 Planarity : 0.004 0.064 3567 Dihedral : 5.007 34.832 2700 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.23 % Allowed : 22.13 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2472 helix: 1.48 (0.21), residues: 594 sheet: -1.31 (0.22), residues: 549 loop : -1.63 (0.17), residues: 1329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3682.58 seconds wall clock time: 68 minutes 47.40 seconds (4127.40 seconds total)